The biggest problem with Dr's 1 and 2 is that about 40% of 1 is missing and 60% of 2 is missing.
Which is why I think #2 is so underrated as the Doctor. His stories and his character were awesome.
What I liked about Sarah and I think what set her apart is that she didn't have a crush on him or look at him as her father or anything, but she was treated as about as equal as the doctor could treat a non-timelord. As was said she was a true 'assistant' helping all the way.
Not really sure I see it the same way although I do see where you're coming from. I thought it very much was a father daughter relationship.